I was not able to reproduce this on mac or windows (with april 23 build)

Maybe I'm not understanding the steps exactly. Here's what I did:

1) download MRHead from SampleData
2) rename to MR.Head
3) all scene files to temp dir

File name is correct as MR.Head.nrrd. MRML scene file saves and reloads correctly. No doubling of the extension is seen either on the file system or inside the MRML file.

Am I messing a step?

I think you're missing a "close scene" --- here's an easier way to reproduce (now using April 23 version on Windows):

• make two copies of the mrhead file (use the file browser, OS level) and name them "MR.head.nrrd" and "MRhead.nrrd" (where ".nrrd" is the file extension)
• start Slicer, "add data" and select one or the other file, then "save"
• then you'll see either of two situations (pics enclosed) depending on that extra dot -- and the extra dot case shows two of the errors (variable name and modified status)
• and if you save the scene you'll see doubling of file extension in the extra dot case, not in the regular case

CaptureDOT.PNG (15,695 bytes)

CaptureNODOT.PNG (16,370 bytes)

Volume storage node was not initialized correctly and therefore failed to strip file extension correctly. Fixed in r27210.

Thanks Andras!